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"Common Characteristic of Sequences of Ribosomal Protein Gene Introns in Saccharomyces cerevisiae". Michal Wolff Advisors: Prof. Martin Kupiec (TAU) DR. Ron Unger. Why? -there is something special about them. Number of intron containing genes = 242 - PowerPoint PPT Presentation
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"Common Characteristic of Sequences of Ribosomal Protein Gene Introns in
Saccharomyces cerevisiae"
Michal WolffAdvisors:Prof. Martin Kupiec (TAU)DR. Ron Unger
Why? -there is something special about them
Number of intron containing genes = 242 Number of ribosomal protein intron containing
genes = 105 = 43% Number of ribosomal protein genes = 140 Ribosomal protein gene introns in the yeast are
larger On average the ribosomal intron length is 405
while the non-ribosomal is 151
Why ?Intron size bias by gene class
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Intron size (bp)
Nu
mb
er o
f in
tro
ns
ribosomal gene introns
non-ribosomal geneintrons
What? - The sequence
homology, consensus, all the intron, areas in the intron, nucleotides.
What? - Secondary structure
Where? - Ares lab Yeast Intron Database
Gene/ORF Name: YMR230W
Description: Small ribosomal subunit protein S10B (rat S10).
Number of introns: 1
Ares Intron Name YMR230W_13_732413_733140_INTRON_53_462
Comments
Length Info (in nt) 410; to Branch base (lariat length) 371
Location relative to orf (nt) start 53; stop 462
Features GUAUGU UUACUAACAAGG AAUAG
Sequence
>YMR230W_13_732417_732466_PREGUUGAUGCCAAAGCAAGAAAGAAACAAAAUUCACCAAUACUUGUUUCAAG>YMR230W_13_732413_733140_INTRON_53_462GUAUGUUUGCAUUUUUUAGGUGAAAUAUGCAGUGAUAUGCUCCGAAAUGGAUAGCAAAGAUGAUAAAUGAAAAUACAAUUAAAUUGAACUUGAAUAUCAUUAAAAGUGGUAGAAAACCGAUUGUUUCAAAAAGAUCUUUGUGGACAAGUACGGCAGUGCAUGAAUCCGAAAGAAAAGUGCAACCUAAGCAGAAUUCCAUUAUUUCACGCGUCCAUUUUUAUAAUGUUUGAACUUUUGAGUCCUUAUAGAAAUGCUAAUAUUAUGAUCAAAGCGAUUAUAUCAUUUACUUUACAGUUUCCGGAGUUUCCGUAUUAUUGCAAAAGGACCACAAACAAUUGAAAUCAUGAUAUCGUAAGAAAUAUUAUUACUAACAAGGAAGAUCAUUGAAUUACGAUCGCAUAUCGAAAUAG>YMR230W_13_732875_732924_POSTAAGGUGUUGUCGUCGCUAAGAAGGAUUUCAACCAAGCUAAGCACGAAGAA
How? – Perl & Bioinformatics Tools
Perl - originally designed for text processing
EMBOSS – sequence alignment mfold – secondary structure BLAST – all against all
How? – Data Analysis
Microsoft Excelchartssortgraphsχ² - expected – non-ribosomal behavior
Results – upstream the intronglutamine
CAA
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nucleotides upstream of the intron
pro
ba
bili
ty
upstream ribosomal intron
upstream non-ribosomal introns
Results – downstream the intronlysine
AAG
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nucleotides downstream of intron
pro
ba
bili
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downstream ribosomal introns
downstreamstream non-ribosomalintrons
Results – in the intron
Hexamers - The biggest difference (30-40%) is in the AU rich sequences for the ribosomal sequences.
Octamer - The ribosomal introns had more poly U octamers then the non-ribosomal ones.
Results - in the intron
10-20 nucleotides upstream from the 3’ end the ribosomal introns have a high probability to contain a polyU sequence.
The area between the branchpoint and the 3’ splice site is around 30 bases long.
UUU,AUU,UUA
Results - in the intronUUU
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area in intron
prob
abili
ty
ribosomal - upstream 3' end
non-ribosomal - upstream 3' end
Results – in the branchpoint-3’
distribution of nucleotides in the branchpoint-3' end area
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10%
20%
30%
40%
50%
60%
nucleotide
pe
rsa
nta
ge
in s
eq
ue
nc
e ribosomal introns
non-ribosomal introns
ribosomal introns 29.80% 12.38% 8.67% 49.15%
non-ribosomal introns 30.53% 16.49% 13.96% 39.02%
A C G U
Results – in the branchpoint-3’
common subsequences A-polyUpolyUpolyU-A
U subsequence with a mutation – In the area – more in the ribosomal introns In the whole intron – more in the non-
ribosomal
Results – in the branchpoint-3’U sequences with one mutation in the intron
and the branchpoint - 3' site area
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sequence length(bp)
pro
ba
bili
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ribosomal introns branchpoint-3' site
non-ribosomal introns branchpoint-3' site
ribosomal introns
non-ribosomal introns
Conclusion
The branchpoint-3’ splice site area might be homologues – all against all blast.
The difference between ribosomal and non-ribosomal may be connected with a polyU sequence.
The ribosomal gene introns and the non-ribosomal gene introns are not similar.
Thanks for listening!